Endurance training represents one extreme in the continuum of skeletal muscle plasticity. The molecular signals elicited in response to acute and chronic exercise and the integration of multiple intracellular pathways are incompletely understood. We determined the effect of 10-d of intensified cycle training on signal transduction in 9 inactive males in response to a 1h acute bout of cycling at the same absolute workload (164±9W). Muscle biopsies were taken at rest, immediately and 3h after the acute exercise. The metabolic signaling pathways including AMPK and mTOR demonstrated divergent regulation by exercise after training. AMPK phosphorylation increased in response to exercise (~16 fold; P<0.05), which was abrogated post training (P<0.01). In contrast mTOR phosphorylation increased in response to exercise (~2 fold; P<0.01), which was augmented post-training (P<0.01) in the presence of increased mTOR expression (P<0.05). Exercise elicited divergent effects on MAPK pathways after training, with exercise-induced ERK1/2 phosphorylation being abolished (P<0.01) and p38 MAPK maintained. Finally, CaMKII exercise-induced phosphorylation and activity were maintained (P<0.01), despite increased expression (~2 fold; P<0.05). In conclusion, 10-d of intensified endurance training attenuated AMPK, ERK1/2 and mTOR, but not CaMKII and p38 MAPK signaling; highlighting molecular pathways important for rapid functional adaptations and maintenance in response to intensified endurance exercise and training.